MVD-tool

Information

A simple C++ parser and tool for the MVD3 and Sonata neuroscience file formats

• provide a tool to convert MVD2 to MVD3
• provide a tool to export MVD to CSV
• provide a simple header base parser for MVD2
• provide a parser based on the HighFive library for MVD3 and Sonata

It also provides a high level Python API for parsing MVD3 and Sonata files.

Compilation

Prerequisites

• CMake >= 3.0
• GCC >= 4.9
• BOOST >= 1.41
• HighFive
• libSONATA

Compile and Install the C++ parser

mkdir build; pushd build
cmake ../ -DCMAKE_INSTALL_PREFIX=<install_dir>
make
make install

Compile and Install the Python API

python setup.py install

Examples with the Python API

Reading Sonata files

import mvdtool
node = mvdtool.open("tests/nodes.h5")
# retrieve data for the full range
node.morphologies()
# retrieve data for a certain range
node.morphologies([0, 1, 3])

Reading MVD3 files

import mvdtool
mvd = mvdtool.open("tests/circuit.mvd3")
mvd.morphologies()

Certain attributes in MVD files require the information from the mecombo file. In this case, it's strictly necessary that the mecombo file contains all combos from the MVD file.

mvd_tsv = mvdtool.open("tests/circuit_tsv.mvd3")
mvd_tsv.open_combo_tsv("tests/mecombo_emodel.tsv")
mvd_tsv.emodels()

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

Copyright © 2015-2022 Blue Brain Project/EPFL

License

LGPLv2.1+